Identification of Genomic Variants of SARS-CoV-2 Using Nanopore Sequencing

Căpraru, Ionuț Dragoș; Romanescu, Mirabela; Anghel, Flavia Medana; Oancea, Cristian; Marian, Cătălin; Sîrbu, Ioan Ovidiu; Chis, Aimee Rodica; Ciordas, Paula Diana

doi:10.3390/medicina58121841

Cited by 5 publications

(2 citation statements)

References 40 publications

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“…The increase in the sensitivity of the diagnostic tests used to detect the presence of the SARS-CoV-2 virus, as well as the decrease in the cost of these determinations, made it possible to identify infected cases with great accuracy [ 20 ]. Normal values of inflammation markers at the time of the first evaluation exclude the presence of an acute infectious and inflammatory process.…”

Section: Discussionmentioning

confidence: 99%

Rhythm Disturbances in Post-Acute COVID-19 Syndrome in Young Men without Pre-Existing Known Cardiovascular Disease—A Case Series

et al. 2023

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Current data indicate the existence of post-acute COVID-19 syndrome frequently expressing as cardiovascular and respiratory health issues. The long-term evolution of these complications is not yet fully known or predictable. Among the most common clinical manifestations of post-acute COVID-19 syndrome are dyspnea, palpitations, and fatigue, in most cases being transient and without underlying any morphological or functional changes. A single-center retrospective observational study was performed on cases that had presented with new-onset cardiac symptoms post-COVID-19 infection. Records of three male patients without pre-existing chronic cardiovascular pathology who had presented for dyspnea, fatigue, and palpitations around four weeks post-COVID-19 acute phase were studied in detail. The three post-COVID-19 cases exhibited arrhythmic complications after completely healing from the acute phase of the infection. Palpitations, along with chest pain, and possible aggravation or appearance of dyspnea, with syncopal episodes, were found to be present. All the three cases were non-vaccinated against COVID-19 infection. Isolated case reports showing arrhythmic complications such as atrial fibrillation and ventricular tachycardia on a small number of patients with these complications indicate the need for arrhythmic evaluation of large groups of patients in the post-acute stage of the COVID-19 syndrome for a better understanding of the phenomenon and implicitly better care of these patients. It would also be useful to evaluate large groups of patients divided into vaccinated/non-vaccinated against COVID-19 categories to determine whether vaccination per se can provide protection in the occurrence of these types of complications.

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Section: Discussionmentioning

confidence: 99%

Rhythm Disturbances in Post-Acute COVID-19 Syndrome in Young Men without Pre-Existing Known Cardiovascular Disease—A Case Series

et al. 2023

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“…There were four groups of patients, according to the period of time they were admitted and the type of virus that was circulating: group 1 (all 2020, original SARS-CoV-2 virus), group 2 (spring 2021, alpha variant), group 3 (autumn 2021, delta variant) and group 4 (spring 2022, delta and omicron variants) (8). There were time intervals (months) between these groups when there were no SARS-CoV-2 positive patients requiring hospital admission.…”

Section: Methodsmentioning

confidence: 99%

COVID-19 in Pregnant Patients at Term: Evolution of Coagulation Factors in Mild Forms throughout the Pandemic: Conventional Analysis and Logistic Regression

Filip

Covali

Socolov

et al. 2023

Maedica

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Aim: The evolution of coagulation factors in pregnant patients infected with SARS-CoV-2 during the pandemic is still debated. However, few studies have been carried out to evaluate the silent alterations of blood values in mild forms of the disease.Methods: A total of 153 pregnant patients with an asymptomatic form of COVID-19 and 306 healthy pregnant patients, who were admitted for delivery in our hospital between April 1, 2020 and March 1, 2022, were studied. The blood values harvested closest to the time of delivery were considered.Results: There was a significant variability in values of fibrinogen, prothrombin time, though these were still within normal limits.Conclusions: Pregnant patients with mild forms of COVID-19 displayed some blood alterations, even if they were asymptomatic for

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Analytical Performance of a Novel Nanopore Sequencing for SARS‐CoV‐2 Genomic Surveillance

Maimaiti,

Kong,

et al. 2024

Journal of Medical Virology

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The genomic analysis of SARS‐CoV‐2 has served as a crucial tool for generating invaluable data that fulfils both epidemiological and clinical necessities. Long‐read sequencing technology (e.g., ONT) has been widely used, providing a real‐time and faster response when necessitated. A novel nanopore‐based long‐read sequencing platform named QNome nanopore has been successfully used for bacterial genome sequencing and assembly; however, its performance in the SARS‐CoV‐2 genomic surveillance is still lacking. Synthetic SARS‐CoV‐2 controls and 120 nasopharyngeal swab (NPS) samples that tested positive by real‐time polymerase chain reaction were sequenced on both QNome and MGI platforms in parallel. The analytical performance of QNome was compared to the short‐read sequencing on MGI. For the synthetic SARS‐CoV‐2 controls, despite the increased error rates observed in QNome nanopore sequencing reads, accurate consensus‐level sequence determination was achieved with an average mapping quality score of approximately 60 (i.e., a mapping accuracy of 99.9999%). For the NPS samples, the average genomic coverage was 89.35% on the QNome nanopore platform compared with 90.39% for MGI. In addition, fewer consensus genomes from QNome were determined to be good by Nextclade compare with MGI (p < 0.05). A total of 9004 mutations were identified using QNome sequencing, with substitutions being the most prevalent, in contrast, 10 997 mutations were detected on MGI (p < 0.05). Furthermore, 23 large deletions (i.e., deletions≥ 10 bp) were identified by QNome while 19/23 were supported by evidence from short‐read sequencing. Phylogenetic analysis revealed that the Pango lineage of consensus genomes for SARS‐CoV‐2 sequenced by QNome concorded 83.04% with MGI. QNome nanopore sequencing, though challenged by read quality and accuracy compared to MGI, is overcoming these issues through bioinformatics and computational advances. The advantage of structure variation (SV) detection capabilities and real‐time data analysis renders it a promising alternative nanopore platform for the surveillance of the SARS‐CoV‐2.

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Identification of Genomic Variants of SARS-CoV-2 Using Nanopore Sequencing

Cited by 5 publications

References 40 publications

Rhythm Disturbances in Post-Acute COVID-19 Syndrome in Young Men without Pre-Existing Known Cardiovascular Disease—A Case Series

Rhythm Disturbances in Post-Acute COVID-19 Syndrome in Young Men without Pre-Existing Known Cardiovascular Disease—A Case Series

COVID-19 in Pregnant Patients at Term: Evolution of Coagulation Factors in Mild Forms throughout the Pandemic: Conventional Analysis and Logistic Regression

Analytical Performance of a Novel Nanopore Sequencing for SARS‐CoV‐2 Genomic Surveillance

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